Data used in this analysis

Specifically, in this experiment set, known experiment labels are:

General description

This report contains all the functional information that was requested by the options when functional_Hunter.R was executed. The functional categories can be:

+ Biological Process + Molecular Function + Cellular Component

All the functional categories are computed with ClusterProfiler and GO categories are computed also with TopGo.

Some sections will not show if there are not sinficative results. Each category is analysed using Over representation analysis (ORA) and Gene Set Analysis (GSEA). The ORA method takes a group of significative DEGs (only DEGs, upregulated DEGs or downregulated DEGs) and performs a hypergeometric test for each term of the selected functional category. In the case of the GSEA method, all the genes are sorted by their fold-change and the algorithm scan which genes with similar fold-change shares a term of the selected functional category.

Statistics about input results obtained from DEGenes Expression Hunter are:

Gene_tag Genes
NOT_DEG 15317
POSSIBLE_DEG 351
PREVALENT_DEG 698

Top genes

Table of signifcant genes. Variables taken into account are being shown into table (except gene symbols/ID). Top of positive (19 items) and negative (16 items) are being shown in two different tables

Top positive

rownames input_IDs logFC_DESeq2 logFC_edgeR mean_logFCs SYMBOL
ENSG00000248752 ENSG00000248752 4.99362884319258 5.92210361914924 5.45786623117091 NA
ENSG00000239503 ENSG00000239503 5.0268612328416 4.78207459342231 4.90446791313196 NA
ENSG00000170522 ENSG00000170522 5.0468950687396 5.97377576624718 5.51033541749339 ELOVL6
ENSG00000106070 ENSG00000106070 5.05115795885436 5.97583685217659 5.51349740551548 GRB10
ENSG00000223525 ENSG00000223525 5.05318450244465 5.97628186669892 5.51473318457179 NA
ENSG00000279996 ENSG00000279996 5.08682391552295 4.83412666675982 4.96047529114139 NA
ENSG00000223646 ENSG00000223646 5.181541803924 6.11128759178856 5.64641469785628 LOC101928012
ENSG00000164120 ENSG00000164120 5.21397804579226 4.96276648304253 5.0883722644174 HPGD
ENSG00000166535 ENSG00000166535 5.71892268680558 5.47079996065518 5.59486132373038 A2ML1
ENSG00000163534 ENSG00000163534 5.76328490012225 5.71115295155166 5.73721892583695 FCRL1
ENSG00000248837 ENSG00000248837 5.96936352182643 6.88447490987186 6.42691921584915 LOC105374524
ENSG00000249948 ENSG00000249948 6.06699164935877 6.98448743939958 6.52573954437917 GBA3
ENSG00000171517 ENSG00000171517 6.28483532162719 7.19780420514928 6.74131976338823 LPAR3
ENSG00000132704 ENSG00000132704 7.02521246130768 7.9331425872725 7.47917752429009 FCRL2
ENSG00000073754 ENSG00000073754 7.61383873767194 7.42080959780015 7.51732416773605 CD5L
ENSG00000277913 ENSG00000277913 4.81277226859045 5.7488517784667 5.28081202352857 NA
ENSG00000224081 ENSG00000224081 4.83203592061477 5.75843026039269 5.29523309050373 NA
ENSG00000271553 ENSG00000271553 4.93748303016735 5.86788360336815 5.40268331676775 NA
ENSG00000233186 ENSG00000233186 4.95334876466837 5.87573792710228 5.41454334588533 KLF4P1

Top negative

rownames input_IDs logFC_DESeq2 logFC_edgeR mean_logFCs SYMBOL
ENSG00000248752 ENSG00000248752 4.99362884319258 5.92210361914924 5.45786623117091 NA
ENSG00000239503 ENSG00000239503 5.0268612328416 4.78207459342231 4.90446791313196 NA
ENSG00000170522 ENSG00000170522 5.0468950687396 5.97377576624718 5.51033541749339 ELOVL6
ENSG00000106070 ENSG00000106070 5.05115795885436 5.97583685217659 5.51349740551548 GRB10
ENSG00000223525 ENSG00000223525 5.05318450244465 5.97628186669892 5.51473318457179 NA
ENSG00000279996 ENSG00000279996 5.08682391552295 4.83412666675982 4.96047529114139 NA
ENSG00000223646 ENSG00000223646 5.181541803924 6.11128759178856 5.64641469785628 LOC101928012
ENSG00000164120 ENSG00000164120 5.21397804579226 4.96276648304253 5.0883722644174 HPGD
ENSG00000166535 ENSG00000166535 5.71892268680558 5.47079996065518 5.59486132373038 A2ML1
ENSG00000163534 ENSG00000163534 5.76328490012225 5.71115295155166 5.73721892583695 FCRL1
ENSG00000248837 ENSG00000248837 5.96936352182643 6.88447490987186 6.42691921584915 LOC105374524
ENSG00000249948 ENSG00000249948 6.06699164935877 6.98448743939958 6.52573954437917 GBA3
ENSG00000171517 ENSG00000171517 6.28483532162719 7.19780420514928 6.74131976338823 LPAR3
ENSG00000132704 ENSG00000132704 7.02521246130768 7.9331425872725 7.47917752429009 FCRL2
ENSG00000073754 ENSG00000073754 7.61383873767194 7.42080959780015 7.51732416773605 CD5L
ENSG00000277913 ENSG00000277913 4.81277226859045 5.7488517784667 5.28081202352857 NA
ENSG00000224081 ENSG00000224081 4.83203592061477 5.75843026039269 5.29523309050373 NA
ENSG00000271553 ENSG00000271553 4.93748303016735 5.86788360336815 5.40268331676775 NA
ENSG00000233186 ENSG00000233186 4.95334876466837 5.87573792710228 5.41454334588533 KLF4P1

Reactome - Over Representation Analysis

The ORA method takes a group of significant genes and performs a Fisher's exact test for each term of the selected functional category.

Barplot

The most highly signficant categories in ascending order, according to adjusted p-value. The x-axis represents the number of significant genes found within the functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Distributions of Log2FC

This plot shows the distribution of gene Log2FC that enriched the top enriched functional term/pathways. The X axis repressent the distribution values. The color of the distribution repressents the FDR of the enrichment. The vertical lines represents the first, second and third quartiles.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

Upsetplot

Genes are clustered according to shared enriched categories. The y-axis shows the number of genes belonging to the different clusters (top) and categories to which they belong (bottom).

KEGG - Over Representation Analysis

The ORA method takes a group of significant genes and performs a Fisher's exact test for each term of the selected functional category.

Barplot

The most highly signficant categories in ascending order, according to adjusted p-value. The x-axis represents the number of significant genes found within the functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Distributions of Log2FC

This plot shows the distribution of gene Log2FC that enriched the top enriched functional term/pathways. The X axis repressent the distribution values. The color of the distribution repressents the FDR of the enrichment. The vertical lines represents the first, second and third quartiles.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

Upsetplot

Genes are clustered according to shared enriched categories. The y-axis shows the number of genes belonging to the different clusters (top) and categories to which they belong (bottom).

BP - Over Representation Analysis

The ORA method takes a group of significant genes and performs a Fisher's exact test for each term of the selected functional category.

Barplot

The most highly signficant categories in ascending order, according to adjusted p-value. The x-axis represents the number of significant genes found within the functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Distributions of Log2FC

This plot shows the distribution of gene Log2FC that enriched the top enriched functional term/pathways. The X axis repressent the distribution values. The color of the distribution repressents the FDR of the enrichment. The vertical lines represents the first, second and third quartiles.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

Upsetplot

Genes are clustered according to shared enriched categories. The y-axis shows the number of genes belonging to the different clusters (top) and categories to which they belong (bottom).

CC - Over Representation Analysis

The ORA method takes a group of significant genes and performs a Fisher's exact test for each term of the selected functional category.

Barplot

The most highly signficant categories in ascending order, according to adjusted p-value. The x-axis represents the number of significant genes found within the functional category.

Dotplot

The most highly signficant categories in descending in categories of gene ratio, defined as the proportion of significant genes that are found in the functional category. The x-axis represents the gene ratio and the dot size the number of genes associated with the functional category.

Distributions of Log2FC

This plot shows the distribution of gene Log2FC that enriched the top enriched functional term/pathways. The X axis repressent the distribution values. The color of the distribution repressents the FDR of the enrichment. The vertical lines represents the first, second and third quartiles.

Gene-Concept Network

The network connects the top functional categories (brown nodes) to their associated genes (grey or colored nodes). The size of the functional category nodes shows the number of connected genes.

Enrich Map plot

The top functional categories (nodes), connected if they share genes. Edge thickness represents the number of shared genes. Nodes size represents the number of significant genes within the category.

Heatplot

Significant genes (x-axis) and the functional categories in which they appear.

Upsetplot

Genes are clustered according to shared enriched categories. The y-axis shows the number of genes belonging to the different clusters (top) and categories to which they belong (bottom).

No ORA enrichment found for MF

BP - Enrichments for Principal Components

Functional enrichments of PCs using all genes


This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs
GO.ID Term positive.PC.1 negative.PC.1 positive.PC.2 negative.PC.2
GO:0002181 cytoplasmic translation 7.28e-19 NA NA NA
GO:0002399 MHC class II protein complex assembly 2.34e-12 NA NA NA
GO:0002503 peptide antigen assembly with MHC class ... 2.34e-12 NA NA NA
GO:0006412 translation 2.79e-11 NA NA NA
GO:0032543 mitochondrial translation 5.54e-08 NA NA NA
GO:0061844 antimicrobial humoral immune response me... 1.44e-06 NA NA NA
GO:0019730 antimicrobial humoral response 1.12e-05 NA NA NA
GO:0140053 mitochondrial gene expression 2.05e-05 NA NA NA
GO:0001906 cell killing 3.00e-05 NA NA NA
GO:0002504 antigen processing and presentation of p... 6.74e-05 NA NA NA
GO:0002495 antigen processing and presentation of p... 1.61e-04 NA NA NA
GO:0006119 oxidative phosphorylation 1.80e-04 NA NA 1.77e-02
GO:0043069 negative regulation of programmed cell d... 2.08e-04 NA NA NA
GO:0006959 humoral immune response 2.08e-04 NA NA NA
GO:0002396 MHC protein complex assembly 2.08e-04 NA NA NA
GO:0002501 peptide antigen assembly with MHC protei... 2.08e-04 NA NA NA
GO:0043066 negative regulation of apoptotic process 4.65e-04 NA NA NA
GO:0048002 antigen processing and presentation of p... 4.90e-04 NA NA NA
GO:0045333 cellular respiration 5.82e-04 NA NA 1.46e-03
GO:0002227 innate immune response in mucosa 6.69e-04 NA NA NA
GO:1990748 cellular detoxification 1.06e-03 NA NA NA
GO:0019538 protein metabolic process 1.06e-03 NA NA NA
GO:0097237 cellular response to toxic substance 1.06e-03 NA NA NA
GO:0019886 antigen processing and presentation of e... 1.09e-03 NA NA NA
GO:0002478 antigen processing and presentation of e... 1.13e-03 NA NA NA
GO:0032353 negative regulation of hormone biosynthe... 1.79e-03 NA NA NA
GO:0002437 inflammatory response to antigenic stimu... 1.79e-03 NA NA NA
GO:0097250 mitochondrial respirasome assembly 1.85e-03 NA NA 1.32e-02
GO:0030162 regulation of proteolysis 2.11e-03 NA NA NA
GO:0019882 antigen processing and presentation 2.11e-03 NA NA NA
GO:0098869 cellular oxidant detoxification 2.93e-03 NA NA NA
GO:2001234 negative regulation of apoptotic signali... 2.99e-03 NA NA NA
GO:0051246 regulation of protein metabolic process 3.80e-03 NA NA NA
GO:0061644 protein localization to CENP-A containin... 3.80e-03 NA NA NA
GO:0097707 ferroptosis 3.80e-03 NA NA NA
GO:0019884 antigen processing and presentation of e... 3.80e-03 NA NA NA
GO:0033108 mitochondrial respiratory chain complex ... 4.02e-03 NA NA 7.20e-03
GO:0009060 aerobic respiration 4.02e-03 NA NA 1.40e-03
GO:0006508 proteolysis 4.02e-03 NA NA NA
GO:2001233 regulation of apoptotic signaling pathwa... 4.11e-03 NA NA NA
GO:0097529 myeloid leukocyte migration 4.11e-03 NA NA NA
GO:0036261 7-methylguanosine cap hypermethylation 4.40e-03 NA NA NA
GO:0002536 respiratory burst involved in inflammato... 4.63e-03 NA NA NA
GO:0110076 negative regulation of ferroptosis 4.94e-03 NA NA NA
GO:2001242 regulation of intrinsic apoptotic signal... 5.15e-03 NA NA NA
GO:2001243 negative regulation of intrinsic apoptot... 5.71e-03 NA NA NA
GO:0022904 respiratory electron transport chain 7.52e-03 NA NA NA
GO:0098754 detoxification 7.52e-03 NA NA NA
GO:0033615 mitochondrial proton-transporting ATP sy... 8.17e-03 NA NA NA
GO:0043461 proton-transporting ATP synthase complex... 8.17e-03 NA NA NA
GO:0006694 steroid biosynthetic process 8.79e-03 NA NA NA
GO:0110075 regulation of ferroptosis 8.80e-03 NA NA NA
GO:0001731 formation of translation preinitiation c... 9.14e-03 NA NA NA
GO:1902624 positive regulation of neutrophil migrat... 9.14e-03 NA NA NA
GO:0007056 spindle assembly involved in female meio... 9.65e-03 NA NA NA
GO:0051604 protein maturation 1.12e-02 NA NA NA
GO:0030163 protein catabolic process 1.13e-02 NA NA NA
GO:0001909 leukocyte mediated cytotoxicity 1.21e-02 NA NA NA
GO:0031640 killing of cells of another organism 1.21e-02 NA NA NA
GO:0141061 disruption of cell in another organism 1.21e-02 NA NA NA
GO:0009636 response to toxic substance 1.24e-02 NA NA NA
GO:0002548 monocyte chemotaxis 1.29e-02 NA NA NA
GO:0051603 proteolysis involved in protein cataboli... 1.30e-02 NA NA NA
GO:0019731 antibacterial humoral response 1.30e-02 NA NA NA
GO:0016126 sterol biosynthetic process 1.30e-02 NA NA NA
GO:0022900 electron transport chain 1.33e-02 NA NA NA
GO:0006121 mitochondrial electron transport, succin... 1.34e-02 NA NA NA
GO:1902622 regulation of neutrophil migration 1.39e-02 NA NA NA
GO:0042773 ATP synthesis coupled electron transport 1.48e-02 NA NA NA
GO:0042775 mitochondrial ATP synthesis coupled elec... 1.48e-02 NA NA NA
GO:1902253 regulation of intrinsic apoptotic signal... 1.66e-02 NA NA NA
GO:0048227 plasma membrane to endosome transport 1.66e-02 NA NA NA
GO:0042110 T cell activation 2.04e-02 NA NA NA
GO:0006839 mitochondrial transport 2.06e-02 NA NA 1.92e-02
GO:0141060 disruption of anatomical structure in an... 2.09e-02 NA NA NA
GO:1901029 negative regulation of mitochondrial out... 2.16e-02 NA NA NA
GO:1901617 organic hydroxy compound biosynthetic pr... 2.29e-02 NA NA NA
GO:0006413 translational initiation 2.32e-02 NA NA NA
GO:0006457 protein folding 2.34e-02 NA NA NA
GO:0097190 apoptotic signaling pathway 2.47e-02 NA NA NA
GO:0002687 positive regulation of leukocyte migrati... 2.48e-02 NA NA NA
GO:1990544 mitochondrial ATP transmembrane transpor... 2.62e-02 NA NA NA
GO:0002861 regulation of inflammatory response to a... 2.62e-02 NA NA NA
GO:0044419 biological process involved in interspec... 2.94e-02 NA NA NA
GO:0050729 positive regulation of inflammatory resp... 3.04e-02 NA NA NA
GO:0006879 intracellular iron ion homeostasis 3.06e-02 NA NA NA
GO:0002835 negative regulation of response to tumor... 3.16e-02 NA NA NA
GO:0002838 negative regulation of immune response t... 3.16e-02 NA NA NA
GO:1901137 carbohydrate derivative biosynthetic pro... 3.23e-02 NA NA 1.12e-03
GO:0052548 regulation of endopeptidase activity 3.24e-02 NA NA NA
GO:1902523 positive regulation of protein K63-linke... 3.33e-02 NA NA NA
GO:0097530 granulocyte migration 3.47e-02 NA NA NA
GO:0002709 regulation of T cell mediated immunity 3.71e-02 NA NA NA
GO:0061077 chaperone-mediated protein folding 3.81e-02 NA NA NA
GO:0034109 homotypic cell-cell adhesion 3.81e-02 NA NA NA
GO:1902956 regulation of mitochondrial electron tra... 3.81e-02 NA NA NA
GO:0019646 aerobic electron transport chain 3.81e-02 NA NA NA
GO:0007005 mitochondrion organization 3.81e-02 NA NA NA
GO:0006754 ATP biosynthetic process 3.81e-02 NA NA 2.52e-02
GO:0061450 trophoblast cell migration 3.81e-02 NA NA NA
GO:1901163 regulation of trophoblast cell migration 3.81e-02 NA NA NA
GO:1903715 regulation of aerobic respiration 3.82e-02 NA NA NA
GO:0043207 response to external biotic stimulus 3.82e-02 NA NA NA
GO:0051707 response to other organism 3.82e-02 NA NA NA
GO:0015980 energy derivation by oxidation of organi... 3.85e-02 NA NA 2.16e-02
GO:1902235 regulation of endoplasmic reticulum stre... 3.88e-02 NA NA NA
GO:0043457 regulation of cellular respiration 3.94e-02 NA NA NA
GO:0002424 T cell mediated immune response to tumor... 3.99e-02 NA NA NA
GO:0007006 mitochondrial membrane organization 4.01e-02 NA NA NA
GO:0052547 regulation of peptidase activity 4.02e-02 NA NA NA
GO:1903003 positive regulation of protein deubiquit... 4.04e-02 NA NA NA
GO:0032733 positive regulation of interleukin-10 pr... 4.25e-02 NA NA NA
GO:0050900 leukocyte migration 4.25e-02 NA NA NA
GO:0002685 regulation of leukocyte migration 4.25e-02 NA NA NA
GO:0007159 leukocyte cell-cell adhesion 4.37e-02 NA NA NA
GO:0030003 intracellular monoatomic cation homeosta... 4.43e-02 NA NA NA
GO:0070431 nucleotide-binding oligomerization domai... 4.47e-02 NA NA NA
GO:1901135 carbohydrate derivative metabolic proces... 4.50e-02 NA NA 5.78e-03
GO:0015986 proton motive force-driven ATP synthesis 4.50e-02 NA NA 3.53e-02
GO:0060264 regulation of respiratory burst involved... 4.52e-02 NA NA NA
GO:0089718 amino acid import across plasma membrane 4.84e-02 NA NA NA
GO:0072677 eosinophil migration 4.86e-02 NA NA NA
GO:0001913 T cell mediated cytotoxicity 4.86e-02 NA NA NA
GO:0032613 interleukin-10 production 4.86e-02 NA NA NA
GO:0032653 regulation of interleukin-10 production 4.86e-02 NA NA NA
GO:0006325 chromatin organization NA 7.31e-11 4.10e-04 NA
GO:0006338 chromatin remodeling NA 5.59e-09 2.11e-03 NA
GO:0051056 regulation of small GTPase mediated sign... NA 6.34e-07 NA NA
GO:0019219 regulation of nucleobase-containing comp... NA 4.60e-05 5.13e-03 NA
GO:0051252 regulation of RNA metabolic process NA 4.60e-05 5.23e-04 NA
GO:0034983 peptidyl-lysine deacetylation NA 4.82e-05 NA NA
GO:0006355 regulation of DNA-templated transcriptio... NA 4.98e-05 1.13e-02 NA
GO:2001141 regulation of RNA biosynthetic process NA 4.98e-05 7.24e-03 NA
GO:0051254 positive regulation of RNA metabolic pro... NA 8.30e-05 1.30e-02 NA
GO:0090304 nucleic acid metabolic process NA 9.15e-05 NA NA
GO:0006351 DNA-templated transcription NA 1.80e-04 2.41e-02 NA
GO:0016043 cellular component organization NA 1.80e-04 1.59e-06 NA
GO:0045935 positive regulation of nucleobase-contai... NA 1.80e-04 NA NA
GO:0045893 positive regulation of DNA-templated tra... NA 2.41e-04 3.68e-02 NA
GO:1902680 positive regulation of RNA biosynthetic ... NA 2.41e-04 3.92e-02 NA
GO:0006366 transcription by RNA polymerase II NA 4.25e-04 1.45e-02 NA
GO:0006357 regulation of transcription by RNA polym... NA 4.46e-04 1.24e-02 NA
GO:0016070 RNA metabolic process NA 8.98e-04 NA NA
GO:0007010 cytoskeleton organization NA 9.37e-04 NA NA
GO:0006974 DNA damage response NA 2.09e-03 NA NA
GO:0009190 cyclic nucleotide biosynthetic process NA 2.44e-03 NA NA
GO:0071840 cellular component organization or bioge... NA 2.44e-03 3.03e-04 NA
GO:0141187 nucleic acid biosynthetic process NA 3.24e-03 NA NA
GO:0006281 DNA repair NA 4.15e-03 NA NA
GO:0006139 nucleobase-containing compound metabolic... NA 4.21e-03 NA NA
GO:0032774 RNA biosynthetic process NA 4.33e-03 NA NA
GO:0048386 positive regulation of retinoic acid rec... NA 5.74e-03 NA NA
GO:0006171 cAMP biosynthetic process NA 5.84e-03 NA NA
GO:0018393 internal peptidyl-lysine acetylation NA 5.97e-03 NA NA
GO:0007264 small GTPase-mediated signal transductio... NA 6.86e-03 NA NA
GO:1902679 negative regulation of RNA biosynthetic ... NA 1.07e-02 NA NA
GO:0045892 negative regulation of DNA-templated tra... NA 1.19e-02 NA NA
GO:0106015 negative regulation of inflammatory resp... NA 1.40e-02 NA NA
GO:0000122 negative regulation of transcription by ... NA 1.45e-02 NA NA
GO:0045934 negative regulation of nucleobase-contai... NA 1.56e-02 NA NA
GO:0034654 nucleobase-containing compound biosynthe... NA 1.85e-02 NA NA
GO:0001957 intramembranous ossification NA 1.89e-02 NA NA
GO:0036072 direct ossification NA 1.89e-02 NA NA
GO:0050794 regulation of cellular process NA 1.97e-02 1.18e-05 NA
GO:1904781 positive regulation of protein localizat... NA 2.00e-02 NA NA
GO:0050770 regulation of axonogenesis NA 2.22e-02 NA NA
GO:0000076 DNA replication checkpoint signaling NA 2.28e-02 NA NA
GO:0000226 microtubule cytoskeleton organization NA 2.80e-02 NA NA
GO:0045944 positive regulation of transcription by ... NA 3.18e-02 9.53e-03 NA
GO:0007507 heart development NA 3.24e-02 NA NA
GO:0090521 podocyte cell migration NA 3.32e-02 NA NA
GO:0016310 phosphorylation NA 3.32e-02 NA NA
GO:0098534 centriole assembly NA 3.63e-02 NA NA
GO:0048856 anatomical structure development NA 3.99e-02 NA NA
GO:1903939 regulation of TORC2 signaling NA 4.26e-02 NA NA
GO:0051253 negative regulation of RNA metabolic pro... NA 4.31e-02 NA NA
GO:0048731 system development NA 4.34e-02 2.24e-02 NA
GO:0046777 protein autophosphorylation NA 4.34e-02 NA NA
GO:0072017 distal tubule development NA 4.34e-02 NA NA
GO:0007275 multicellular organism development NA 4.56e-02 2.10e-02 NA
GO:0010468 regulation of gene expression NA 4.68e-02 2.22e-03 NA
GO:0065007 biological regulation NA NA 4.49e-06 NA
GO:0050789 regulation of biological process NA NA 9.85e-06 NA
GO:0016192 vesicle-mediated transport NA NA 1.84e-05 NA
GO:0051649 establishment of localization in cell NA NA 4.77e-05 NA
GO:0051641 cellular localization NA NA 6.45e-05 NA
GO:0007033 vacuole organization NA NA 1.69e-04 NA
GO:0070925 organelle assembly NA NA 3.29e-04 NA
GO:0033036 macromolecule localization NA NA 5.23e-04 NA
GO:0051128 regulation of cellular component organiz... NA NA 5.23e-04 NA
GO:0048523 negative regulation of cellular process NA NA 5.23e-04 NA
GO:0044088 regulation of vacuole organization NA NA 5.56e-04 NA
GO:0070727 cellular macromolecule localization NA NA 6.24e-04 NA
GO:0046907 intracellular transport NA NA 8.56e-04 NA
GO:0015031 protein transport NA NA 8.56e-04 NA
GO:0008104 protein localization NA NA 8.82e-04 NA
GO:0051130 positive regulation of cellular componen... NA NA 9.34e-04 NA
GO:0031323 regulation of cellular metabolic process NA NA 1.06e-03 NA
GO:0010743 regulation of macrophage derived foam ce... NA NA 1.25e-03 NA
GO:0019222 regulation of metabolic process NA NA 1.30e-03 NA
GO:0016050 vesicle organization NA NA 1.46e-03 NA
GO:0006996 organelle organization NA NA 2.05e-03 NA
GO:0048519 negative regulation of biological proces... NA NA 2.11e-03 NA
GO:0060255 regulation of macromolecule metabolic pr... NA NA 2.24e-03 NA
GO:0120036 plasma membrane bounded cell projection ... NA NA 3.34e-03 NA
GO:2000785 regulation of autophagosome assembly NA NA 3.34e-03 NA
GO:0060271 cilium assembly NA NA 4.00e-03 NA
GO:0010556 regulation of macromolecule biosynthetic... NA NA 4.06e-03 NA
GO:0046856 phosphatidylinositol dephosphorylation NA NA 4.06e-03 NA
GO:0045184 establishment of protein localization NA NA 4.06e-03 NA
GO:0030030 cell projection organization NA NA 4.31e-03 NA
GO:0071705 nitrogen compound transport NA NA 4.40e-03 NA
GO:0009889 regulation of biosynthetic process NA NA 5.13e-03 NA
GO:0051129 negative regulation of cellular componen... NA NA 5.13e-03 NA
GO:0046348 amino sugar catabolic process NA NA 5.72e-03 NA
GO:0016197 endosomal transport NA NA 5.72e-03 NA
GO:0000910 cytokinesis NA NA 5.72e-03 NA
GO:0007034 vacuolar transport NA NA 6.02e-03 NA
GO:0031326 regulation of cellular biosynthetic proc... NA NA 6.31e-03 NA
GO:0022607 cellular component assembly NA NA 6.52e-03 NA
GO:0044248 cellular catabolic process NA NA 6.78e-03 NA
GO:0010256 endomembrane system organization NA NA 6.78e-03 NA
GO:0120031 plasma membrane bounded cell projection ... NA NA 7.24e-03 NA
GO:0006886 intracellular protein transport NA NA 7.24e-03 NA
GO:0080090 regulation of primary metabolic process NA NA 1.07e-02 NA
GO:0044782 cilium organization NA NA 1.07e-02 NA
GO:1902115 regulation of organelle assembly NA NA 1.10e-02 NA
GO:0030031 cell projection assembly NA NA 1.17e-02 NA
GO:0033043 regulation of organelle organization NA NA 1.39e-02 NA
GO:1905037 autophagosome organization NA NA 1.45e-02 NA
GO:0048609 multicellular organismal reproductive pr... NA NA 1.46e-02 NA
GO:0007626 locomotory behavior NA NA 1.46e-02 NA
GO:0006914 autophagy NA NA 1.46e-02 NA
GO:0061919 process utilizing autophagic mechanism NA NA 1.46e-02 NA
GO:0099003 vesicle-mediated transport in synapse NA NA 1.46e-02 NA
GO:0007030 Golgi organization NA NA 1.51e-02 NA
GO:0061512 protein localization to cilium NA NA 1.53e-02 NA
GO:0061640 cytoskeleton-dependent cytokinesis NA NA 1.68e-02 NA
GO:0031324 negative regulation of cellular metaboli... NA NA 1.70e-02 NA
GO:0007041 lysosomal transport NA NA 1.70e-02 NA
GO:0010638 positive regulation of organelle organiz... NA NA 1.80e-02 NA
GO:0014059 regulation of dopamine secretion NA NA 1.83e-02 NA
GO:0010629 negative regulation of gene expression NA NA 1.87e-02 NA
GO:0009892 negative regulation of metabolic process NA NA 1.87e-02 NA
GO:0007040 lysosome organization NA NA 1.87e-02 NA
GO:0080171 lytic vacuole organization NA NA 1.87e-02 NA
GO:0007254 JNK cascade NA NA 1.87e-02 NA
GO:0048193 Golgi vesicle transport NA NA 2.00e-02 NA
GO:0048699 generation of neurons NA NA 2.06e-02 NA
GO:0007017 microtubule-based process NA NA 2.11e-02 NA
GO:0007610 behavior NA NA 2.12e-02 NA
GO:0051179 localization NA NA 2.12e-02 NA
GO:2000270 negative regulation of fibroblast apopto... NA NA 2.12e-02 NA
GO:0000281 mitotic cytokinesis NA NA 2.13e-02 NA
GO:0033365 protein localization to organelle NA NA 2.21e-02 NA
GO:0019953 sexual reproduction NA NA 2.41e-02 NA
GO:1905515 non-motile cilium assembly NA NA 2.52e-02 NA
GO:0010745 negative regulation of macrophage derive... NA NA 2.59e-02 NA
GO:1902902 negative regulation of autophagosome ass... NA NA 2.59e-02 NA
GO:0010605 negative regulation of macromolecule met... NA NA 2.61e-02 NA
GO:0009896 positive regulation of catabolic process NA NA 2.83e-02 NA
GO:0007276 gamete generation NA NA 2.83e-02 NA
GO:1901072 glucosamine-containing compound cataboli... NA NA 2.84e-02 NA
GO:0090025 regulation of monocyte chemotaxis NA NA 2.85e-02 NA
GO:0006892 post-Golgi vesicle-mediated transport NA NA 2.85e-02 NA
GO:0051650 establishment of vesicle localization NA NA 2.98e-02 NA
GO:0016236 macroautophagy NA NA 3.00e-02 NA
GO:0000045 autophagosome assembly NA NA 3.03e-02 NA
GO:0051648 vesicle localization NA NA 3.07e-02 NA
GO:0051177 meiotic sister chromatid cohesion NA NA 3.15e-02 NA
GO:0022008 neurogenesis NA NA 3.18e-02 NA
GO:0010558 negative regulation of macromolecule bio... NA NA 3.26e-02 NA
GO:0009894 regulation of catabolic process NA NA 3.36e-02 NA
GO:0036289 peptidyl-serine autophosphorylation NA NA 3.58e-02 NA
GO:1903421 regulation of synaptic vesicle recycling NA NA 3.68e-02 NA
GO:0072001 renal system development NA NA 3.92e-02 NA
GO:0007059 chromosome segregation NA NA 3.92e-02 NA
GO:0022402 cell cycle process NA NA 4.07e-02 NA
GO:0000425 pexophagy NA NA 4.14e-02 NA
GO:0060914 heart formation NA NA 4.14e-02 NA
GO:0099504 synaptic vesicle cycle NA NA 4.19e-02 NA
GO:0048666 neuron development NA NA 4.20e-02 NA
GO:0007283 spermatogenesis NA NA 4.20e-02 NA
GO:0021953 central nervous system neuron differenti... NA NA 4.31e-02 NA
GO:0048468 cell development NA NA 4.34e-02 NA
GO:0007049 cell cycle NA NA 4.49e-02 NA
GO:0090026 positive regulation of monocyte chemotax... NA NA 4.50e-02 NA
GO:0031327 negative regulation of cellular biosynth... NA NA 4.50e-02 NA
GO:0010742 macrophage derived foam cell differentia... NA NA 4.50e-02 NA
GO:0001822 kidney development NA NA 4.71e-02 NA
GO:0048232 male gamete generation NA NA 4.77e-02 NA
GO:0042254 ribosome biogenesis NA NA NA 2.93e-04
GO:0016072 rRNA metabolic process NA NA NA 2.93e-04
GO:0000727 double-strand break repair via break-ind... NA NA NA 5.10e-04
GO:0044281 small molecule metabolic process NA NA NA 5.10e-04
GO:0006753 nucleoside phosphate metabolic process NA NA NA 5.10e-04
GO:0055086 nucleobase-containing small molecule met... NA NA NA 5.10e-04
GO:0006364 rRNA processing NA NA NA 5.10e-04
GO:0009260 ribonucleotide biosynthetic process NA NA NA 5.31e-04
GO:0022613 ribonucleoprotein complex biogenesis NA NA NA 5.31e-04
GO:0009142 nucleoside triphosphate biosynthetic pro... NA NA NA 1.12e-03
GO:0046390 ribose phosphate biosynthetic process NA NA NA 1.12e-03
GO:0017004 cytochrome complex assembly NA NA NA 1.14e-03
GO:0009117 nucleotide metabolic process NA NA NA 1.17e-03
GO:0009141 nucleoside triphosphate metabolic proces... NA NA NA 1.44e-03
GO:0006091 generation of precursor metabolites and ... NA NA NA 1.46e-03
GO:0009199 ribonucleoside triphosphate metabolic pr... NA NA NA 1.46e-03
GO:0009201 ribonucleoside triphosphate biosynthetic... NA NA NA 1.72e-03
GO:0170036 import into the mitochondrion NA NA NA 2.12e-03
GO:0009205 purine ribonucleoside triphosphate metab... NA NA NA 2.74e-03
GO:0019677 NAD catabolic process NA NA NA 2.74e-03
GO:0009259 ribonucleotide metabolic process NA NA NA 2.97e-03
GO:0006399 tRNA metabolic process NA NA NA 3.02e-03
GO:0009144 purine nucleoside triphosphate metabolic... NA NA NA 3.02e-03
GO:0019693 ribose phosphate metabolic process NA NA NA 3.02e-03
GO:1901293 nucleoside phosphate biosynthetic proces... NA NA NA 3.02e-03
GO:0006560 proline metabolic process NA NA NA 3.13e-03
GO:0009152 purine ribonucleotide biosynthetic proce... NA NA NA 3.27e-03
GO:0006735 NADH regeneration NA NA NA 3.27e-03
GO:0061621 canonical glycolysis NA NA NA 3.27e-03
GO:0061718 glucose catabolic process to pyruvate NA NA NA 3.27e-03
GO:0003084 positive regulation of systemic arterial... NA NA NA 3.30e-03
GO:0046034 ATP metabolic process NA NA NA 3.53e-03
GO:0009206 purine ribonucleoside triphosphate biosy... NA NA NA 3.87e-03
GO:0008033 tRNA processing NA NA NA 4.45e-03
GO:0019637 organophosphate metabolic process NA NA NA 4.90e-03
GO:0061620 glycolytic process through glucose-6-pho... NA NA NA 5.31e-03
GO:0009145 purine nucleoside triphosphate biosynthe... NA NA NA 5.32e-03
GO:0009165 nucleotide biosynthetic process NA NA NA 5.32e-03
GO:0072521 purine-containing compound metabolic pro... NA NA NA 5.98e-03
GO:0006271 DNA strand elongation involved in DNA re... NA NA NA 7.78e-03
GO:0006220 pyrimidine nucleotide metabolic process NA NA NA 8.76e-03
GO:0033617 mitochondrial cytochrome c oxidase assem... NA NA NA 9.24e-03
GO:0006270 DNA replication initiation NA NA NA 1.08e-02
GO:0009150 purine ribonucleotide metabolic process NA NA NA 1.09e-02
GO:0009148 pyrimidine nucleoside triphosphate biosy... NA NA NA 1.37e-02
GO:0042274 ribosomal small subunit biogenesis NA NA NA 1.43e-02
GO:0009147 pyrimidine nucleoside triphosphate metab... NA NA NA 1.43e-02
GO:0072527 pyrimidine-containing compound metabolic... NA NA NA 1.43e-02
GO:0061615 glycolytic process through fructose-6-ph... NA NA NA 1.43e-02
GO:0009219 pyrimidine deoxyribonucleotide metabolic... NA NA NA 1.48e-02
GO:0006561 proline biosynthetic process NA NA NA 1.58e-02
GO:0055129 L-proline biosynthetic process NA NA NA 1.58e-02
GO:0009220 pyrimidine ribonucleotide biosynthetic p... NA NA NA 1.61e-02
GO:0072522 purine-containing compound biosynthetic ... NA NA NA 1.77e-02
GO:1990542 mitochondrial transmembrane transport NA NA NA 1.77e-02
GO:0006261 DNA-templated DNA replication NA NA NA 1.87e-02
GO:0030174 regulation of DNA-templated DNA replicat... NA NA NA 2.20e-02
GO:1902075 cellular response to salt NA NA NA 2.20e-02
GO:1903935 response to sodium arsenite NA NA NA 2.20e-02
GO:1903936 cellular response to sodium arsenite NA NA NA 2.20e-02
GO:0008535 respiratory chain complex IV assembly NA NA NA 2.20e-02
GO:0090407 organophosphate biosynthetic process NA NA NA 2.28e-02
GO:0006163 purine nucleotide metabolic process NA NA NA 2.29e-02
GO:0006268 DNA unwinding involved in DNA replicatio... NA NA NA 2.50e-02
GO:0006164 purine nucleotide biosynthetic process NA NA NA 2.98e-02
GO:0043414 macromolecule methylation NA NA NA 2.98e-02
GO:0090329 regulation of DNA-templated DNA replicat... NA NA NA 3.04e-02
GO:0044283 small molecule biosynthetic process NA NA NA 3.22e-02
GO:0009218 pyrimidine ribonucleotide metabolic proc... NA NA NA 3.55e-02
GO:0010155 regulation of proton transport NA NA NA 4.38e-02
GO:0006066 alcohol metabolic process NA NA NA 4.55e-02

Functional enrichments of HCPC clusters using all genes

This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters
GO.ID Term Cluster 1 Cluster 2 Cluster 3
GO:0006261 DNA-templated DNA replication NA 4.5e-02 NA
GO:0002181 cytoplasmic translation NA NA 1.74e-02

Functional enrichments of PCs using only DEGs


This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs
GO.ID Term positive.PC.1 negative.PC.1 positive.PC.2 negative.PC.2
GO:0032787 monocarboxylic acid metabolic process 1.76e-18 NA NA NA
GO:0006631 fatty acid metabolic process 2.73e-18 NA NA NA
GO:0051607 defense response to virus 2.73e-18 NA NA NA
GO:0016053 organic acid biosynthetic process 2.73e-18 NA NA NA
GO:0046394 carboxylic acid biosynthetic process 2.73e-18 NA NA NA
GO:0006082 organic acid metabolic process 3.89e-18 NA NA NA
GO:0043436 oxoacid metabolic process 3.89e-18 NA NA NA
GO:0016197 endosomal transport 5.01e-18 NA NA NA
GO:0006633 fatty acid biosynthetic process 1.44e-17 NA NA NA
GO:0072330 monocarboxylic acid biosynthetic process 1.44e-17 NA NA NA
GO:0019752 carboxylic acid metabolic process 1.45e-17 NA NA NA
GO:0009615 response to virus 2.30e-17 NA NA NA
GO:0008610 lipid biosynthetic process 1.39e-16 NA NA NA
GO:0033559 unsaturated fatty acid metabolic process 5.28e-16 NA NA NA
GO:2001233 regulation of apoptotic signaling pathwa... 3.77e-15 NA NA NA
GO:0016055 Wnt signaling pathway 1.36e-14 NA NA NA
GO:0030111 regulation of Wnt signaling pathway 1.36e-14 NA NA NA
GO:0006886 intracellular protein transport 1.36e-14 NA NA NA
GO:2001234 negative regulation of apoptotic signali... 1.83e-14 NA NA NA
GO:0044089 positive regulation of cellular componen... 3.29e-14 NA NA NA
GO:0002495 antigen processing and presentation of p... 4.78e-14 NA NA NA
GO:0002504 antigen processing and presentation of p... 4.78e-14 NA NA NA
GO:0019886 antigen processing and presentation of e... 4.78e-14 NA NA NA
GO:0030335 positive regulation of cell migration 1.16e-13 NA NA NA
GO:2000147 positive regulation of cell motility 1.16e-13 NA NA NA
GO:1990845 adaptive thermogenesis 1.65e-13 NA NA NA
GO:0001906 cell killing 4.08e-13 NA NA NA
GO:0030334 regulation of cell migration 4.67e-13 NA NA NA
GO:2000145 regulation of cell motility 4.67e-13 NA NA NA
GO:0050821 protein stabilization 6.15e-13 NA NA NA
GO:0006790 sulfur compound metabolic process 1.09e-12 NA NA NA
GO:0072594 establishment of protein localization to... 1.10e-12 NA NA NA
GO:0019884 antigen processing and presentation of e... 1.60e-12 NA NA NA
GO:0070201 regulation of establishment of protein l... 1.67e-12 NA NA NA
GO:0097193 intrinsic apoptotic signaling pathway 2.95e-12 NA NA NA
GO:0002697 regulation of immune effector process 5.83e-12 NA NA NA
GO:0001659 temperature homeostasis 7.98e-12 NA NA NA
GO:0002478 antigen processing and presentation of e... 1.23e-11 NA NA NA
GO:0048002 antigen processing and presentation of p... 1.23e-11 NA NA NA
GO:0097529 myeloid leukocyte migration 1.45e-11 NA NA NA
GO:1904951 positive regulation of establishment of ... 1.51e-11 NA NA NA
GO:2001236 regulation of extrinsic apoptotic signal... 2.43e-11 NA NA NA
GO:0002263 cell activation involved in immune respo... 1.78e-10 NA NA NA
GO:0002366 leukocyte activation involved in immune ... 1.78e-10 NA NA NA
GO:0019079 viral genome replication 1.96e-10 NA NA NA
GO:0097530 granulocyte migration 2.52e-10 NA NA NA
GO:0007169 cell surface receptor protein tyrosine k... 2.53e-10 NA NA NA
GO:0002274 myeloid leukocyte activation 2.99e-10 NA NA NA
GO:0006694 steroid biosynthetic process 4.78e-10 NA NA NA
GO:0006937 regulation of muscle contraction 5.00e-10 NA NA NA
GO:0030595 leukocyte chemotaxis 5.33e-10 NA NA NA
GO:0019216 regulation of lipid metabolic process 9.33e-10 NA NA NA
GO:0071621 granulocyte chemotaxis 9.33e-10 NA NA NA
GO:2001242 regulation of intrinsic apoptotic signal... 1.44e-09 NA NA NA
GO:0002526 acute inflammatory response 1.44e-09 NA NA NA
GO:0052548 regulation of endopeptidase activity 1.48e-09 NA NA NA
GO:0031960 response to corticosteroid 2.09e-09 NA NA NA
GO:0051384 response to glucocorticoid 2.09e-09 NA NA NA
GO:0048608 reproductive structure development 2.09e-09 NA NA NA
GO:0061458 reproductive system development 2.09e-09 NA NA NA
GO:0051223 regulation of protein transport 2.64e-09 NA NA NA
GO:0097191 extrinsic apoptotic signaling pathway 3.84e-09 NA NA NA
GO:2001243 negative regulation of intrinsic apoptot... 6.26e-09 NA NA NA
GO:0090407 organophosphate biosynthetic process 1.08e-08 NA NA NA
GO:1904062 regulation of monoatomic cation transmem... 1.54e-08 NA NA NA
GO:0001763 morphogenesis of a branching structure 2.65e-08 NA NA NA
GO:0061138 morphogenesis of a branching epithelium 2.65e-08 NA NA NA
GO:0007565 female pregnancy 4.22e-08 NA NA NA
GO:0044703 multi-organism reproductive process 4.22e-08 NA NA NA
GO:0044706 multi-multicellular organism process 4.22e-08 NA NA NA
GO:0032970 regulation of actin filament-based proce... 7.41e-08 NA NA NA
GO:0031640 killing of cells of another organism 7.41e-08 NA NA NA
GO:0141060 disruption of anatomical structure in an... 7.41e-08 NA NA NA
GO:0141061 disruption of cell in another organism 7.41e-08 NA NA NA
GO:0010810 regulation of cell-substrate adhesion 7.71e-08 NA NA NA
GO:1990266 neutrophil migration 9.69e-08 NA NA NA
GO:0051222 positive regulation of protein transport 1.23e-07 NA NA NA
GO:0045766 positive regulation of angiogenesis 3.97e-07 NA NA NA
GO:1904018 positive regulation of vasculature devel... 3.97e-07 NA NA NA
GO:0032388 positive regulation of intracellular tra... 7.88e-07 NA NA NA
GO:0070371 ERK1 and ERK2 cascade 1.26e-06 NA NA NA
GO:0050727 regulation of inflammatory response 1.37e-06 NA NA NA
GO:0001890 placenta development 1.98e-06 NA NA NA
GO:0010951 negative regulation of endopeptidase act... 2.64e-06 NA NA NA
GO:1901342 regulation of vasculature development 3.03e-06 NA NA NA
GO:0006605 protein targeting 8.33e-06 NA NA NA
GO:0015850 organic hydroxy compound transport 1.17e-05 NA NA NA
GO:0006869 lipid transport 1.69e-05 NA NA NA
GO:0010876 lipid localization 1.69e-05 NA NA NA
GO:0043281 regulation of cysteine-type endopeptidas... 2.24e-05 NA NA NA
GO:2000116 regulation of cysteine-type endopeptidas... 2.24e-05 NA NA NA
GO:0034764 positive regulation of transmembrane tra... 4.62e-05 NA NA NA
GO:0006575 cellular modified amino acid metabolic p... 6.22e-05 NA NA NA
GO:0045765 regulation of angiogenesis 6.58e-05 NA NA NA
GO:0050673 epithelial cell proliferation 8.58e-05 NA NA NA
GO:0050678 regulation of epithelial cell proliferat... 8.58e-05 NA NA NA
GO:0033077 T cell differentiation in thymus 1.07e-04 NA NA NA
GO:0032956 regulation of actin cytoskeleton organiz... 1.81e-04 NA NA NA
GO:0048754 branching morphogenesis of an epithelial... 2.50e-04 NA NA NA
GO:1902903 regulation of supramolecular fiber organ... 2.59e-04 NA NA NA
GO:0045165 cell fate commitment 3.21e-04 NA NA NA
GO:0098739 import across plasma membrane 3.26e-04 NA NA NA
GO:0040013 negative regulation of locomotion 7.06e-04 NA NA NA
GO:2000146 negative regulation of cell motility 7.06e-04 NA NA NA
GO:0110053 regulation of actin filament organizatio... 2.88e-03 NA NA NA
GO:0097190 apoptotic signaling pathway 6.92e-03 NA NA NA
GO:0006954 inflammatory response 1.49e-02 NA NA NA
GO:0040012 regulation of locomotion 1.62e-02 NA NA NA
GO:0043069 negative regulation of programmed cell d... 2.13e-02 NA NA NA
GO:0006952 defense response 2.52e-02 NA NA NA
GO:0006955 immune response 2.72e-02 NA NA NA
GO:0098657 import into cell 2.91e-02 NA NA NA
GO:0043066 negative regulation of apoptotic process 3.52e-02 NA NA NA
GO:0097237 cellular response to toxic substance NA NA 7.18e-04 NA
GO:0098754 detoxification NA NA 7.18e-04 NA
GO:1990748 cellular detoxification NA NA 7.18e-04 NA
GO:1901888 regulation of cell junction assembly NA NA 3.41e-02 NA
GO:0048513 animal organ development NA NA NA 2.73e-02
GO:0032502 developmental process NA NA NA 2.73e-02
GO:0048856 anatomical structure development NA NA NA 4.63e-02
GO:0009653 anatomical structure morphogenesis NA NA NA 4.63e-02

Functional enrichments of HCPC clusters using only DEGs


This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters
GO.ID Term Cluster 1 Cluster 2 Cluster 3
GO:0006091 generation of precursor metabolites and ... 7.63e-05 NA NA
GO:2001236 regulation of extrinsic apoptotic signal... 1.52e-04 NA NA
GO:0071356 cellular response to tumor necrosis fact... 4.59e-04 NA NA
GO:0008380 RNA splicing 4.59e-04 NA NA
GO:0051302 regulation of cell division 5.74e-04 NA NA
GO:0097435 supramolecular fiber organization 9.09e-03 NA NA

CC - Enrichments for Principal Components

Functional enrichments of PCs using all genes


This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs
GO.ID Term positive.PC.1 negative.PC.1 positive.PC.2 negative.PC.2
GO:0022625 cytosolic large ribosomal subunit 2.16e-74 NA NA 4.93e-03
GO:0044391 ribosomal subunit 1.54e-45 NA NA 4.50e-03
GO:0005840 ribosome 3.83e-30 NA NA 3.45e-02
GO:0022626 cytosolic ribosome 1.03e-29 NA NA NA
GO:0070062 extracellular exosome 1.64e-29 NA NA NA
GO:1903561 extracellular vesicle 1.64e-29 NA NA NA
GO:0015934 large ribosomal subunit 1.64e-29 NA NA 4.50e-03
GO:0043230 extracellular organelle 1.64e-29 NA NA NA
GO:0065010 extracellular membrane-bounded organelle 1.64e-29 NA NA NA
GO:0005615 extracellular space 1.22e-25 NA NA NA
GO:0005576 extracellular region 3.53e-24 NA NA NA
GO:0022627 cytosolic small ribosomal subunit 4.72e-19 NA NA NA
GO:0015935 small ribosomal subunit 7.37e-17 NA NA NA
GO:0042613 MHC class II protein complex 3.05e-15 NA NA NA
GO:0031982 vesicle 4.38e-14 NA NA NA
GO:0005783 endoplasmic reticulum 1.45e-12 NA NA NA
GO:1990904 ribonucleoprotein complex 5.72e-10 NA NA 1.43e-02
GO:0005789 endoplasmic reticulum membrane 5.88e-10 NA NA NA
GO:0098827 endoplasmic reticulum subcompartment 6.50e-10 NA NA NA
GO:0031090 organelle membrane 8.02e-10 NA NA NA
GO:0042175 nuclear outer membrane-endoplasmic retic... 1.03e-09 NA NA NA
GO:0042611 MHC protein complex 1.67e-09 NA NA NA
GO:0098796 membrane protein complex 2.00e-09 NA NA NA
GO:0098798 mitochondrial protein-containing complex 3.04e-09 NA NA 4.27e-03
GO:0019866 organelle inner membrane 4.29e-09 NA NA 4.31e-10
GO:0005743 mitochondrial inner membrane 1.10e-08 NA NA 1.12e-10
GO:0005740 mitochondrial envelope 2.45e-08 NA NA 1.07e-06
GO:0000313 organellar ribosome 3.09e-08 NA NA NA
GO:0005761 mitochondrial ribosome 3.09e-08 NA NA NA
GO:0031966 mitochondrial membrane 3.91e-08 NA NA 3.38e-06
GO:0030141 secretory granule 9.01e-08 NA NA NA
GO:0000315 organellar large ribosomal subunit 2.98e-07 NA NA NA
GO:0005762 mitochondrial large ribosomal subunit 2.98e-07 NA NA NA
GO:0140534 endoplasmic reticulum protein-containing... 2.40e-06 NA NA NA
GO:0012505 endomembrane system 2.44e-06 NA NA NA
GO:0005739 mitochondrion 3.09e-06 NA NA 6.32e-07
GO:0005925 focal adhesion 5.13e-06 NA NA 4.58e-02
GO:0099503 secretory vesicle 5.14e-06 NA NA NA
GO:0031984 organelle subcompartment 6.66e-06 NA NA NA
GO:0030055 cell-substrate junction 6.66e-06 NA NA 4.58e-02
GO:0031967 organelle envelope 1.01e-05 NA NA 2.78e-03
GO:0016020 membrane 1.29e-05 NA NA NA
GO:0005766 primary lysosome 2.07e-05 NA NA NA
GO:0042582 azurophil granule 2.07e-05 NA NA NA
GO:0005839 proteasome core complex 3.25e-05 NA NA NA
GO:0030662 coated vesicle membrane 4.93e-05 NA NA NA
GO:0005834 heterotrimeric G-protein complex 5.09e-05 NA NA NA
GO:0030134 COPII-coated ER to Golgi transport vesic... 6.60e-05 NA NA NA
GO:0120115 Lsm2-8 complex 7.76e-05 NA NA NA
GO:0005683 U7 snRNP 8.94e-05 NA NA NA
GO:0035577 azurophil granule membrane 9.27e-05 NA NA NA
GO:0032991 protein-containing complex 9.27e-05 NA NA NA
GO:0042470 melanosome 1.32e-04 NA NA NA
GO:0048770 pigment granule 1.32e-04 NA NA NA
GO:0030135 coated vesicle 2.72e-04 NA NA NA
GO:0012507 ER to Golgi transport vesicle membrane 2.72e-04 NA NA NA
GO:0005787 signal peptidase complex 3.03e-04 NA NA NA
GO:0043505 CENP-A containing nucleosome 3.03e-04 NA NA NA
GO:0061638 CENP-A containing chromatin 3.03e-04 NA NA NA
GO:0000323 lytic vacuole 3.29e-04 NA 1.57e-03 NA
GO:0005764 lysosome 3.29e-04 NA 1.57e-03 NA
GO:1990726 Lsm1-7-Pat1 complex 4.12e-04 NA NA NA
GO:0000139 Golgi membrane 4.64e-04 NA NA NA
GO:0098553 lumenal side of endoplasmic reticulum me... 4.86e-04 NA NA NA
GO:0098556 cytoplasmic side of rough endoplasmic re... 5.04e-04 NA NA NA
GO:0000314 organellar small ribosomal subunit 6.90e-04 NA NA NA
GO:0005763 mitochondrial small ribosomal subunit 6.90e-04 NA NA NA
GO:0000502 proteasome complex 6.90e-04 NA NA NA
GO:0030133 transport vesicle 8.53e-04 NA 1.57e-03 NA
GO:0031983 vesicle lumen 8.54e-04 NA NA NA
GO:0060205 cytoplasmic vesicle lumen 8.54e-04 NA NA NA
GO:0098552 side of membrane 8.54e-04 NA NA NA
GO:0030667 secretory granule membrane 8.99e-04 NA NA NA
GO:0098588 bounding membrane of organelle 9.58e-04 NA NA NA
GO:0098803 respiratory chain complex 9.58e-04 NA NA 5.15e-03
GO:0005759 mitochondrial matrix 9.88e-04 NA NA 4.56e-04
GO:1905360 GTPase complex 9.88e-04 NA NA NA
GO:0034774 secretory granule lumen 9.99e-04 NA NA NA
GO:0001772 immunological synapse 1.31e-03 NA NA NA
GO:1905369 endopeptidase complex 1.35e-03 NA NA NA
GO:0008250 oligosaccharyltransferase complex 1.64e-03 NA NA NA
GO:0031902 late endosome membrane 1.70e-03 NA 2.51e-03 NA
GO:0019773 proteasome core complex, alpha-subunit c... 1.84e-03 NA NA NA
GO:0009986 cell surface 1.85e-03 NA NA NA
GO:0098857 membrane microdomain 1.87e-03 NA NA NA
GO:0030669 clathrin-coated endocytic vesicle membra... 1.89e-03 NA NA NA
GO:0016469 proton-transporting two-sector ATPase co... 1.92e-03 NA NA NA
GO:0030666 endocytic vesicle membrane 2.58e-03 NA NA NA
GO:0070820 tertiary granule 3.00e-03 NA NA NA
GO:0045121 membrane raft 3.47e-03 NA NA NA
GO:0005775 vacuolar lumen 3.48e-03 NA NA NA
GO:0043227 membrane-bounded organelle 3.49e-03 NA NA NA
GO:0005773 vacuole 4.00e-03 NA 4.50e-04 NA
GO:0000786 nucleosome 4.09e-03 NA 6.00e-05 NA
GO:0097197 tetraspanin-enriched microdomain 4.42e-03 NA NA NA
GO:0030670 phagocytic vesicle membrane 4.61e-03 NA NA NA
GO:0030659 cytoplasmic vesicle membrane 4.88e-03 NA NA NA
GO:0101002 ficolin-1-rich granule 4.88e-03 NA NA NA
GO:0034715 pICln-Sm protein complex 4.88e-03 NA NA NA
GO:0043231 intracellular membrane-bounded organelle 5.67e-03 NA NA NA
GO:0005791 rough endoplasmic reticulum 6.67e-03 NA NA NA
GO:0030665 clathrin-coated vesicle membrane 6.67e-03 NA NA NA
GO:0005737 cytoplasm 6.93e-03 NA NA NA
GO:0098576 lumenal side of membrane 6.94e-03 NA NA NA
GO:0012506 vesicle membrane 7.79e-03 NA NA NA
GO:0031410 cytoplasmic vesicle 8.24e-03 NA NA NA
GO:0017059 serine palmitoyltransferase complex 9.28e-03 NA NA NA
GO:1904813 ficolin-1-rich granule lumen 9.33e-03 NA NA NA
GO:1904724 tertiary granule lumen 9.44e-03 NA NA NA
GO:0072562 blood microparticle 9.75e-03 NA NA NA
GO:0005885 Arp2/3 protein complex 9.98e-03 NA NA NA
GO:1990351 transporter complex 1.08e-02 NA NA NA
GO:0045334 clathrin-coated endocytic vesicle 1.08e-02 NA NA NA
GO:0005758 mitochondrial intermembrane space 1.08e-02 NA NA NA
GO:0097708 intracellular vesicle 1.13e-02 NA NA NA
GO:0009897 external side of plasma membrane 1.29e-02 NA NA NA
GO:0005688 U6 snRNP 1.30e-02 NA NA NA
GO:0090533 cation-transporting ATPase complex 1.30e-02 NA NA NA
GO:0005765 lysosomal membrane 1.37e-02 NA 4.12e-02 NA
GO:0098852 lytic vacuole membrane 1.37e-02 NA 4.12e-02 NA
GO:0001405 PAM complex, Tim23 associated import mot... 1.40e-02 NA NA NA
GO:0045335 phagocytic vesicle 1.42e-02 NA NA NA
GO:0034506 chromosome, centromeric core domain 1.69e-02 NA NA NA
GO:0005838 proteasome regulatory particle 1.81e-02 NA NA NA
GO:0002178 palmitoyltransferase complex 1.81e-02 NA NA NA
GO:0033178 proton-transporting two-sector ATPase co... 1.89e-02 NA NA NA
GO:0005744 TIM23 mitochondrial import inner membran... 1.90e-02 NA NA 2.16e-02
GO:0031234 extrinsic component of cytoplasmic side ... 2.05e-02 NA NA NA
GO:0033116 endoplasmic reticulum-Golgi intermediate... 2.05e-02 NA NA NA
GO:0071204 histone pre-mRNA 3'end processing comple... 2.07e-02 NA NA NA
GO:0005774 vacuolar membrane 2.19e-02 NA 1.80e-02 NA
GO:0019774 proteasome core complex, beta-subunit co... 2.25e-02 NA NA NA
GO:0035578 azurophil granule lumen 2.32e-02 NA NA NA
GO:1902495 transmembrane transporter complex 2.37e-02 NA NA NA
GO:0030663 COPI-coated vesicle membrane 2.56e-02 NA NA NA
GO:0030658 transport vesicle membrane 2.63e-02 NA 3.22e-02 NA
GO:0140596 TOM complex 2.77e-02 NA NA NA
GO:0098797 plasma membrane protein complex 2.77e-02 NA NA NA
GO:1905368 peptidase complex 2.79e-02 NA NA NA
GO:0030867 rough endoplasmic reticulum membrane 2.79e-02 NA NA NA
GO:0008290 F-actin capping protein complex 2.82e-02 NA NA NA
GO:0072546 EMC complex 2.83e-02 NA NA NA
GO:0042612 MHC class I protein complex 2.90e-02 NA NA NA
GO:0070993 translation preinitiation complex 3.28e-02 NA NA NA
GO:0031970 organelle envelope lumen 3.30e-02 NA NA NA
GO:0005798 Golgi-associated vesicle 3.46e-02 NA NA NA
GO:0071007 U2-type catalytic step 2 spliceosome 4.13e-02 NA NA NA
GO:0030136 clathrin-coated vesicle 4.30e-02 NA NA NA
GO:0032040 small-subunit processome 4.36e-02 NA NA 2.32e-02
GO:0098800 inner mitochondrial membrane protein com... 4.41e-02 NA NA 5.15e-03
GO:0033176 proton-transporting V-type ATPase comple... 4.71e-02 NA NA NA
GO:0005856 cytoskeleton NA 1.54e-05 2.00e-02 NA
GO:0015630 microtubule cytoskeleton NA 5.63e-04 3.10e-04 NA
GO:0005815 microtubule organizing center NA 1.41e-03 9.51e-04 NA
GO:0043194 axon initial segment NA 1.92e-03 NA NA
GO:0005694 chromosome NA 2.18e-03 4.29e-03 NA
GO:0005814 centriole NA 2.26e-03 2.97e-03 NA
GO:0036064 ciliary basal body NA 2.91e-03 NA NA
GO:0016604 nuclear body NA 3.27e-03 1.73e-04 NA
GO:0043228 non-membrane-bounded organelle NA 4.33e-03 NA NA
GO:0043232 intracellular non-membrane-bounded organ... NA 4.33e-03 NA NA
GO:0016607 nuclear speck NA 5.48e-03 1.57e-03 NA
GO:0031931 TORC1 complex NA 5.98e-03 NA NA
GO:0042995 cell projection NA 7.30e-03 NA NA
GO:0034451 centriolar satellite NA 8.58e-03 NA NA
GO:0120025 plasma membrane bounded cell projection NA 1.09e-02 NA NA
GO:0097427 microtubule bundle NA 1.09e-02 NA NA
GO:0000785 chromatin NA 1.10e-02 1.93e-03 NA
GO:0099738 cell cortex region NA 1.22e-02 NA NA
GO:0035097 histone methyltransferase complex NA 1.24e-02 NA NA
GO:0032437 cuticular plate NA 2.12e-02 NA NA
GO:0048786 presynaptic active zone NA 2.15e-02 NA NA
GO:0035976 transcription factor AP-1 complex NA 2.27e-02 NA NA
GO:0043005 neuron projection NA 2.83e-02 NA NA
GO:0005813 centrosome NA 4.26e-02 5.60e-05 NA
GO:0000776 kinetochore NA NA 2.70e-05 NA
GO:0000775 chromosome, centromeric region NA NA 2.70e-05 NA
GO:0000779 condensed chromosome, centromeric region NA NA 2.70e-05 NA
GO:0005770 late endosome NA NA 3.10e-04 NA
GO:0000922 spindle pole NA NA 9.34e-04 NA
GO:0005768 endosome NA NA 1.57e-03 NA
GO:0010008 endosome membrane NA NA 1.57e-03 NA
GO:0005829 cytosol NA NA 1.57e-03 NA
GO:0005769 early endosome NA NA 1.57e-03 NA
GO:0005819 spindle NA NA 1.57e-03 NA
GO:0031901 early endosome membrane NA NA 1.57e-03 NA
GO:0005622 intracellular anatomical structure NA NA 2.16e-03 NA
GO:0005802 trans-Golgi network NA NA 2.16e-03 NA
GO:0000793 condensed chromosome NA NA 2.34e-03 NA
GO:0008021 synaptic vesicle NA NA 2.58e-03 NA
GO:0008278 cohesin complex NA NA 3.46e-03 NA
GO:0005634 nucleus NA NA 4.94e-03 NA
GO:0098793 presynapse NA NA 5.47e-03 NA
GO:0098791 Golgi apparatus subcompartment NA NA 6.43e-03 NA
GO:0098687 chromosomal region NA NA 7.71e-03 NA
GO:0005942 phosphatidylinositol 3-kinase complex NA NA 1.19e-02 NA
GO:0070382 exocytic vesicle NA NA 1.54e-02 NA
GO:0030892 mitotic cohesin complex NA NA 1.82e-02 NA
GO:0030496 midbody NA NA 3.13e-02 NA
GO:0035032 phosphatidylinositol 3-kinase complex, c... NA NA 3.13e-02 NA
GO:0000407 phagophore assembly site NA NA 3.13e-02 NA
GO:0005794 Golgi apparatus NA NA 3.22e-02 NA
GO:0008024 cyclin/CDK positive transcription elonga... NA NA 3.22e-02 NA
GO:0030672 synaptic vesicle membrane NA NA 3.58e-02 NA
GO:0099501 exocytic vesicle membrane NA NA 3.58e-02 NA
GO:0110165 cellular anatomical entity NA NA 4.05e-02 NA
GO:0098850 extrinsic component of synaptic vesicle ... NA NA 4.12e-02 NA
GO:0071162 CMG complex NA NA NA 1.00e-04
GO:0031261 DNA replication preinitiation complex NA NA NA 2.37e-03
GO:0030684 preribosome NA NA NA 7.03e-03
GO:0001931 uropod NA NA NA 1.08e-02
GO:1990204 oxidoreductase complex NA NA NA 1.36e-02
GO:0070069 cytochrome complex NA NA NA 3.11e-02
GO:0001725 stress fiber NA NA NA 3.29e-02
GO:0097517 contractile actin filament bundle NA NA NA 3.29e-02
GO:0005658 alpha DNA polymerase:primase complex NA NA NA 4.04e-02

Functional enrichments of HCPC clusters using all genes

This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters
GO.ID Term Cluster 1 Cluster 2 Cluster 3
GO:0022626 cytosolic ribosome NA NA 2.91e-05
GO:0044391 ribosomal subunit NA NA 3.85e-04
GO:0022625 cytosolic large ribosomal subunit NA NA 3.85e-04
GO:0031982 vesicle NA NA 3.85e-04
GO:0005773 vacuole NA NA 3.85e-04
GO:0012505 endomembrane system NA NA 3.85e-04
GO:1903561 extracellular vesicle NA NA 3.85e-04
GO:0043230 extracellular organelle NA NA 3.85e-04
GO:0065010 extracellular membrane-bounded organelle NA NA 3.85e-04
GO:0000323 lytic vacuole NA NA 3.85e-04
GO:0005764 lysosome NA NA 3.85e-04
GO:0005783 endoplasmic reticulum NA NA 4.74e-04
GO:0005576 extracellular region NA NA 5.49e-04
GO:0070062 extracellular exosome NA NA 5.91e-04
GO:0000775 chromosome, centromeric region NA NA 8.03e-04
GO:0005615 extracellular space NA NA 9.05e-04
GO:0005840 ribosome NA NA 1.18e-03
GO:0000786 nucleosome NA NA 1.28e-03
GO:0042175 nuclear outer membrane-endoplasmic retic... NA NA 1.74e-03
GO:0022627 cytosolic small ribosomal subunit NA NA 2.00e-03
GO:0005789 endoplasmic reticulum membrane NA NA 3.37e-03
GO:0098827 endoplasmic reticulum subcompartment NA NA 3.73e-03
GO:0031984 organelle subcompartment NA NA 4.05e-03
GO:0000793 condensed chromosome NA NA 4.05e-03
GO:0098588 bounding membrane of organelle NA NA 5.03e-03
GO:0015935 small ribosomal subunit NA NA 5.20e-03
GO:0030133 transport vesicle NA NA 6.03e-03
GO:0005770 late endosome NA NA 9.06e-03
GO:0031902 late endosome membrane NA NA 1.13e-02
GO:0030867 rough endoplasmic reticulum membrane NA NA 1.59e-02
GO:0005774 vacuolar membrane NA NA 1.59e-02
GO:0005737 cytoplasm NA NA 2.07e-02
GO:0015934 large ribosomal subunit NA NA 2.31e-02
GO:0005791 rough endoplasmic reticulum NA NA 2.39e-02
GO:0097708 intracellular vesicle NA NA 2.39e-02
GO:0031410 cytoplasmic vesicle NA NA 2.46e-02
GO:0000779 condensed chromosome, centromeric region NA NA 2.89e-02
GO:0031090 organelle membrane NA NA 2.89e-02
GO:0042611 MHC protein complex NA NA 3.35e-02
GO:0000776 kinetochore NA NA 3.35e-02
GO:0000139 Golgi membrane NA NA 3.49e-02
GO:0005775 vacuolar lumen NA NA 3.71e-02
GO:0000502 proteasome complex NA NA 3.77e-02
GO:0099503 secretory vesicle NA NA 3.92e-02
GO:0098796 membrane protein complex NA NA 4.49e-02
GO:0005765 lysosomal membrane NA NA 4.74e-02
GO:0098852 lytic vacuole membrane NA NA 4.74e-02

Functional enrichments of PCs using only DEGs


This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs
GO.ID Term positive.PC.1 negative.PC.1 positive.PC.2 negative.PC.2
GO:0005740 mitochondrial envelope 2.82e-23 NA NA NA
GO:0031966 mitochondrial membrane 2.82e-23 NA NA NA
GO:0031967 organelle envelope 6.76e-23 NA NA NA
GO:0005743 mitochondrial inner membrane 7.81e-23 NA NA NA
GO:0019866 organelle inner membrane 1.61e-22 NA NA NA
GO:0005770 late endosome 1.69e-22 NA NA NA
GO:0030662 coated vesicle membrane 1.55e-21 NA NA NA
GO:0031902 late endosome membrane 1.66e-21 NA NA NA
GO:0005759 mitochondrial matrix 2.43e-20 NA NA NA
GO:0043202 lysosomal lumen 2.27e-19 NA NA NA
GO:0012507 ER to Golgi transport vesicle membrane 8.70e-19 NA NA NA
GO:0030665 clathrin-coated vesicle membrane 1.86e-18 NA NA NA
GO:0032588 trans-Golgi network membrane 8.24e-18 NA NA NA
GO:0030669 clathrin-coated endocytic vesicle membra... 9.00e-16 NA NA NA
GO:0045334 clathrin-coated endocytic vesicle 9.00e-16 NA NA NA
GO:0030666 endocytic vesicle membrane 1.02e-15 NA NA NA
GO:0042611 MHC protein complex 1.23e-12 NA NA NA
GO:0042613 MHC class II protein complex 1.23e-12 NA NA NA
GO:0098553 lumenal side of endoplasmic reticulum me... 1.23e-12 NA NA NA
GO:0098576 lumenal side of membrane 1.23e-12 NA NA NA
GO:0005635 nuclear envelope 8.10e-11 NA NA NA
GO:0016363 nuclear matrix 5.15e-10 NA NA NA
GO:0000793 condensed chromosome 3.83e-06 NA NA NA
GO:0005739 mitochondrion 1.46e-03 NA NA NA
GO:0005765 lysosomal membrane 1.09e-02 NA NA NA
GO:0005774 vacuolar membrane 1.09e-02 NA NA NA
GO:0098852 lytic vacuole membrane 1.09e-02 NA NA NA
GO:0005768 endosome 3.77e-02 NA NA NA
GO:0071944 cell periphery NA NA NA 4.00e-04
GO:0005886 plasma membrane NA NA NA 1.38e-03
GO:0098590 plasma membrane region NA NA NA 3.48e-02
GO:0005911 cell-cell junction NA NA NA 3.48e-02

Functional enrichments of HCPC clusters using only DEGs


This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters
GO.ID Term Cluster 1 Cluster 2 Cluster 3
GO:0005766 primary lysosome 8.69e-06 NA NA
GO:0042582 azurophil granule 8.69e-06 NA NA
GO:0005667 transcription regulator complex 1.40e-05 NA NA
GO:0090575 RNA polymerase II transcription regulato... 1.69e-05 NA NA
GO:0099081 supramolecular polymer 3.71e-03 NA NA
GO:0099512 supramolecular fiber 3.71e-03 NA NA
GO:0005856 cytoskeleton 8.51e-03 NA NA
GO:0016607 nuclear speck 1.23e-02 NA NA
GO:0030863 cortical cytoskeleton 3.90e-02 NA NA
GO:0036477 somatodendritic compartment 3.90e-02 NA NA
GO:0015629 actin cytoskeleton 3.96e-02 NA NA
GO:0030864 cortical actin cytoskeleton 4.47e-02 NA NA
GO:0043228 non-membrane-bounded organelle 4.47e-02 NA NA
GO:0043232 intracellular non-membrane-bounded organ... 4.47e-02 NA NA
GO:0030054 cell junction 4.83e-02 NA NA

MF - Enrichments for Principal Components

Functional enrichments of PCs using all genes


This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs
GO.ID Term positive.PC.1 negative.PC.1 positive.PC.2 negative.PC.2
GO:0003735 structural constituent of ribosome 1.53e-42 NA NA 2.75e-03
GO:0005198 structural molecule activity 3.23e-11 NA NA NA
GO:0023026 MHC class II protein complex binding 3.23e-11 NA NA NA
GO:0019843 rRNA binding 5.65e-09 NA NA NA
GO:0003924 GTPase activity 4.71e-08 NA NA NA
GO:0030527 structural constituent of chromatin 1.82e-07 NA 1.82e-03 NA
GO:0032395 MHC class II receptor activity 2.21e-07 NA NA NA
GO:0023023 MHC protein complex binding 5.95e-06 NA NA NA
GO:0019001 guanyl nucleotide binding 1.31e-05 NA NA NA
GO:0032561 guanyl ribonucleotide binding 1.31e-05 NA NA NA
GO:0005525 GTP binding 1.64e-05 NA NA NA
GO:0051920 peroxiredoxin activity 2.34e-05 NA NA NA
GO:0097177 mitochondrial ribosome binding 4.55e-05 NA NA NA
GO:0008379 thioredoxin peroxidase activity 5.19e-05 NA NA NA
GO:0140824 thioredoxin-dependent peroxiredoxin acti... 5.19e-05 NA NA NA
GO:0019003 GDP binding 5.41e-05 NA NA NA
GO:0003925 G protein activity 7.26e-05 NA NA NA
GO:0046982 protein heterodimerization activity 2.16e-04 NA NA NA
GO:0016209 antioxidant activity 2.87e-04 NA NA NA
GO:0042605 peptide antigen binding 6.09e-04 NA NA NA
GO:0003823 antigen binding 1.16e-03 NA NA NA
GO:0008430 selenium binding 1.60e-03 NA NA NA
GO:0042287 MHC protein binding 1.89e-03 NA NA NA
GO:0003723 RNA binding 2.65e-03 NA NA NA
GO:0061650 ubiquitin-like protein conjugating enzym... 2.91e-03 NA NA NA
GO:0140375 immune receptor activity 2.93e-03 NA NA NA
GO:0042277 peptide binding 3.38e-03 NA NA NA
GO:0005125 cytokine activity 3.40e-03 NA NA NA
GO:0031681 G-protein beta-subunit binding 3.40e-03 NA NA NA
GO:0019788 NEDD8 transferase activity 4.26e-03 NA NA NA
GO:0004601 peroxidase activity 6.56e-03 NA NA NA
GO:1903136 cuprous ion binding 6.84e-03 NA NA NA
GO:0016684 oxidoreductase activity, acting on perox... 7.25e-03 NA NA NA
GO:0004930 G protein-coupled receptor activity 7.76e-03 NA NA NA
GO:0031386 protein tag activity 1.02e-02 NA NA NA
GO:0141047 molecular tag activity 1.02e-02 NA NA NA
GO:0003743 translation initiation factor activity 1.02e-02 NA NA NA
GO:0016615 malate dehydrogenase activity 1.02e-02 NA NA NA
GO:0061134 peptidase regulator activity 1.02e-02 NA NA NA
GO:0048027 mRNA 5'-UTR binding 1.02e-02 NA NA NA
GO:0004866 endopeptidase inhibitor activity 1.28e-02 NA NA NA
GO:0098632 cell-cell adhesion mediator activity 1.35e-02 NA NA NA
GO:0044183 protein folding chaperone 1.62e-02 NA NA NA
GO:0061631 ubiquitin conjugating enzyme activity 1.78e-02 NA NA NA
GO:0045296 cadherin binding 1.79e-02 NA NA NA
GO:0086080 protein binding involved in heterotypic ... 1.98e-02 NA NA NA
GO:0140678 molecular function inhibitor activity 1.98e-02 NA NA NA
GO:0032977 membrane insertase activity 1.98e-02 NA NA NA
GO:0070700 BMP receptor binding 1.98e-02 NA NA NA
GO:0016494 C-X-C chemokine receptor activity 2.02e-02 NA NA NA
GO:0048018 receptor ligand activity 2.30e-02 NA NA NA
GO:0001609 G protein-coupled adenosine receptor act... 2.57e-02 NA NA NA
GO:0030545 signaling receptor regulator activity 2.68e-02 NA NA NA
GO:0008097 5S rRNA binding 2.71e-02 NA NA NA
GO:0046983 protein dimerization activity 2.77e-02 NA NA NA
GO:0051087 protein-folding chaperone binding 2.77e-02 NA NA NA
GO:0004954 prostanoid receptor activity 2.77e-02 NA NA NA
GO:0004955 prostaglandin receptor activity 2.77e-02 NA NA NA
GO:0030414 peptidase inhibitor activity 2.77e-02 NA NA NA
GO:0009055 electron transfer activity 3.30e-02 NA NA NA
GO:0008603 cAMP-dependent protein kinase regulator ... 3.83e-02 NA NA NA
GO:0055102 lipase inhibitor activity 4.11e-02 NA NA NA
GO:0008020 G protein-coupled photoreceptor activity 4.19e-02 NA NA NA
GO:0016491 oxidoreductase activity 4.19e-02 NA NA 4.73e-02
GO:0030546 signaling receptor activator activity 4.58e-02 NA NA NA
GO:0050839 cell adhesion molecule binding 4.93e-02 NA NA NA
GO:0005524 ATP binding NA 8.80e-19 NA NA
GO:0032559 adenyl ribonucleotide binding NA 9.02e-19 NA NA
GO:0030554 adenyl nucleotide binding NA 4.17e-18 NA NA
GO:0030695 GTPase regulator activity NA 4.40e-14 4.34e-02 NA
GO:0060589 nucleoside-triphosphatase regulator acti... NA 4.40e-14 4.34e-02 NA
GO:0005096 GTPase activator activity NA 5.33e-14 1.68e-02 NA
GO:0016773 phosphotransferase activity, alcohol gro... NA 3.29e-13 NA NA
GO:0043167 ion binding NA 3.59e-13 NA NA
GO:0016301 kinase activity NA 1.37e-12 NA NA
GO:0016772 transferase activity, transferring phosp... NA 1.82e-12 NA NA
GO:0140993 histone modifying activity NA 5.46e-12 NA NA
GO:0004672 protein kinase activity NA 1.68e-11 NA NA
GO:0036094 small molecule binding NA 3.60e-11 NA NA
GO:0106310 protein serine kinase activity NA 2.35e-09 NA NA
GO:0004674 protein serine/threonine kinase activity NA 3.19e-09 NA NA
GO:0140030 modification-dependent protein binding NA 1.02e-08 NA NA
GO:0043168 anion binding NA 2.68e-08 NA NA
GO:0046872 metal ion binding NA 3.10e-08 NA NA
GO:0043169 cation binding NA 4.84e-08 NA NA
GO:0032553 ribonucleotide binding NA 5.01e-08 NA NA
GO:0035639 purine ribonucleoside triphosphate bindi... NA 5.80e-08 NA NA
GO:0032555 purine ribonucleotide binding NA 8.08e-08 NA NA
GO:0017076 purine nucleotide binding NA 1.56e-07 NA NA
GO:0042393 histone binding NA 1.69e-07 NA NA
GO:0016887 ATP hydrolysis activity NA 7.79e-07 NA NA
GO:1901363 heterocyclic compound binding NA 8.76e-07 NA NA
GO:0004386 helicase activity NA 1.42e-06 NA NA
GO:0000166 nucleotide binding NA 1.42e-06 NA NA
GO:1901265 nucleoside phosphate binding NA 1.67e-06 NA NA
GO:0003677 DNA binding NA 2.70e-06 2.80e-02 NA
GO:0003682 chromatin binding NA 2.89e-06 NA NA
GO:0005085 guanyl-nucleotide exchange factor activi... NA 3.99e-06 NA NA
GO:0140657 ATP-dependent activity NA 5.69e-06 NA NA
GO:0035173 histone kinase activity NA 5.89e-06 NA NA
GO:0097367 carbohydrate derivative binding NA 6.36e-06 NA NA
GO:0044024 histone H2AS1 kinase activity NA 9.90e-06 NA NA
GO:0140995 histone H2A kinase activity NA 9.90e-06 NA NA
GO:0035091 phosphatidylinositol binding NA 3.22e-05 NA NA
GO:0005543 phospholipid binding NA 6.09e-05 NA NA
GO:0035064 methylated histone binding NA 9.51e-05 NA NA
GO:0140034 methylation-dependent protein binding NA 9.67e-05 NA NA
GO:0016740 transferase activity NA 9.67e-05 NA NA
GO:0140947 histone H3K9me2 methyltransferase activi... NA 1.02e-04 NA NA
GO:0140096 catalytic activity, acting on a protein NA 1.49e-04 NA NA
GO:0031267 small GTPase binding NA 1.93e-04 2.24e-02 NA
GO:0140110 transcription regulator activity NA 2.07e-04 NA NA
GO:0046976 histone H3K27 methyltransferase activity NA 2.78e-04 NA NA
GO:0140938 histone H3 methyltransferase activity NA 3.00e-04 NA NA
GO:0043565 sequence-specific DNA binding NA 3.89e-04 NA NA
GO:0042054 histone methyltransferase activity NA 4.29e-04 NA NA
GO:0140097 catalytic activity, acting on DNA NA 4.29e-04 NA NA
GO:0051020 GTPase binding NA 4.74e-04 NA NA
GO:0008289 lipid binding NA 5.29e-04 NA NA
GO:0140033 acetylation-dependent protein binding NA 7.95e-04 NA NA
GO:0140999 histone H3K4 trimethyltransferase activi... NA 8.93e-04 NA NA
GO:0004713 protein tyrosine kinase activity NA 1.08e-03 NA NA
GO:0070577 lysine-acetylated histone binding NA 1.51e-03 NA NA
GO:0140939 histone H4 methyltransferase activity NA 1.60e-03 NA NA
GO:0008094 ATP-dependent activity, acting on DNA NA 1.67e-03 NA NA
GO:0004445 inositol-polyphosphate 5-phosphatase act... NA 1.91e-03 NA NA
GO:0004683 calcium/calmodulin-dependent protein kin... NA 1.91e-03 NA NA
GO:0009374 biotin binding NA 1.93e-03 NA NA
GO:0008381 mechanosensitive monoatomic ion channel ... NA 1.99e-03 NA NA
GO:0004016 adenylate cyclase activity NA 2.37e-03 NA NA
GO:0003712 transcription coregulator activity NA 2.40e-03 NA NA
GO:0140640 catalytic activity, acting on a nucleic ... NA 2.45e-03 NA NA
GO:0003690 double-stranded DNA binding NA 2.67e-03 NA NA
GO:0008047 enzyme activator activity NA 2.67e-03 4.17e-02 NA
GO:1990837 sequence-specific double-stranded DNA bi... NA 3.64e-03 NA NA
GO:0030674 protein-macromolecule adaptor activity NA 4.46e-03 NA NA
GO:0097159 organic cyclic compound binding NA 4.88e-03 NA NA
GO:0016279 protein-lysine N-methyltransferase activ... NA 6.19e-03 NA NA
GO:0140457 protein demethylase activity NA 6.31e-03 2.83e-03 NA
GO:0016849 phosphorus-oxygen lyase activity NA 6.80e-03 NA NA
GO:0000976 transcription cis-regulatory region bind... NA 7.84e-03 NA NA
GO:0008170 N-methyltransferase activity NA 8.65e-03 NA NA
GO:0001067 transcription regulatory region nucleic ... NA 8.66e-03 NA NA
GO:0016278 lysine N-methyltransferase activity NA 1.03e-02 NA NA
GO:0032452 histone demethylase activity NA 1.13e-02 2.98e-03 NA
GO:0016741 transferase activity, transferring one-c... NA 1.16e-02 NA NA
GO:0010484 histone H3 acetyltransferase activity NA 1.20e-02 NA NA
GO:0060090 molecular adaptor activity NA 1.35e-02 NA NA
GO:0008276 protein methyltransferase activity NA 1.38e-02 NA NA
GO:0140658 ATP-dependent chromatin remodeler activi... NA 1.40e-02 NA NA
GO:0052658 inositol-1,4,5-trisphosphate 5-phosphata... NA 1.51e-02 NA NA
GO:0046030 inositol trisphosphate phosphatase activ... NA 1.54e-02 NA NA
GO:0071889 14-3-3 protein binding NA 1.61e-02 NA NA
GO:0003950 NAD+-protein poly-ADP-ribosyltransferase... NA 1.75e-02 NA NA
GO:0008168 methyltransferase activity NA 1.90e-02 NA NA
GO:0052659 inositol-1,3,4,5-tetrakisphosphate 5-pho... NA 1.90e-02 NA NA
GO:0003824 catalytic activity NA 1.97e-02 NA NA
GO:0031701 angiotensin receptor binding NA 2.10e-02 NA NA
GO:0016706 2-oxoglutarate-dependent dioxygenase act... NA 2.14e-02 NA NA
GO:0003713 transcription coactivator activity NA 2.14e-02 NA NA
GO:0015276 ligand-gated monoatomic ion channel acti... NA 2.14e-02 NA NA
GO:0008186 ATP-dependent activity, acting on RNA NA 2.15e-02 NA NA
GO:0005516 calmodulin binding NA 2.15e-02 NA NA
GO:0048407 platelet-derived growth factor binding NA 2.26e-02 NA NA
GO:0022834 ligand-gated channel activity NA 2.26e-02 NA NA
GO:0001409 guanine nucleotide transmembrane transpo... NA 2.28e-02 NA NA
GO:0022836 gated channel activity NA 2.28e-02 NA NA
GO:0141052 histone H3 demethylase activity NA 2.33e-02 1.82e-03 NA
GO:0003678 DNA helicase activity NA 2.68e-02 NA NA
GO:0036408 histone H3K14 acetyltransferase activity NA 2.75e-02 NA NA
GO:0141039 phosphatidylinositol 3-kinase inhibitor ... NA 2.89e-02 NA NA
GO:0043139 5'-3' DNA helicase activity NA 3.10e-02 NA NA
GO:0008349 MAP kinase kinase kinase kinase activity NA 3.10e-02 NA NA
GO:0016273 arginine N-methyltransferase activity NA 3.10e-02 NA NA
GO:0016274 protein-arginine N-methyltransferase act... NA 3.10e-02 NA NA
GO:0008017 microtubule binding NA 3.10e-02 3.24e-03 NA
GO:0140566 histone reader activity NA 3.11e-02 NA NA
GO:0099094 ligand-gated monoatomic cation channel a... NA 3.41e-02 NA NA
GO:0003724 RNA helicase activity NA 3.41e-02 NA NA
GO:0009975 cyclase activity NA 3.49e-02 NA NA
GO:0003774 cytoskeletal motor activity NA 3.56e-02 NA NA
GO:0008757 S-adenosylmethionine-dependent methyltra... NA 3.60e-02 NA NA
GO:1901981 phosphatidylinositol phosphate binding NA 3.98e-02 NA NA
GO:0042800 histone H3K4 methyltransferase activity NA 4.23e-02 NA NA
GO:0033558 protein lysine deacetylase activity NA 4.89e-02 NA NA
GO:0004712 protein serine/threonine/tyrosine kinase... NA 4.89e-02 NA NA
GO:0000149 SNARE binding NA NA 2.83e-03 NA
GO:0015631 tubulin binding NA NA 2.83e-03 NA
GO:0032454 histone H3K9 demethylase activity NA NA 2.83e-03 NA
GO:0005488 binding NA NA 9.42e-03 NA
GO:0046914 transition metal ion binding NA NA 1.56e-02 NA
GO:0008270 zinc ion binding NA NA 1.68e-02 NA
GO:0019783 ubiquitin-like protein peptidase activit... NA NA 1.68e-02 NA
GO:0032451 demethylase activity NA NA 1.93e-02 NA
GO:0043394 proteoglycan binding NA NA 2.03e-02 NA
GO:0004843 cysteine-type deubiquitinase activity NA NA 2.11e-02 NA
GO:0051864 histone H3K36 demethylase activity NA NA 3.53e-02 NA
GO:0101005 deubiquitinase activity NA NA 3.61e-02 NA
GO:0035242 protein-arginine omega-N asymmetric meth... NA NA NA 3.13e-02
GO:0001054 RNA polymerase I activity NA NA NA 3.37e-02

Functional enrichments of HCPC clusters using all genes

This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters
GO.ID Term Cluster 1 Cluster 2 Cluster 3
GO:0004239 initiator methionyl aminopeptidase activ... 3.45e-02 NA NA
GO:0030554 adenyl nucleotide binding NA 1.17e-05 NA
GO:0005524 ATP binding NA 1.47e-05 NA
GO:0032559 adenyl ribonucleotide binding NA 1.47e-05 NA
GO:0016772 transferase activity, transferring phosp... NA 5.29e-04 NA
GO:0016773 phosphotransferase activity, alcohol gro... NA 1.44e-03 NA
GO:0016301 kinase activity NA 1.59e-03 NA
GO:0140993 histone modifying activity NA 5.73e-03 NA
GO:1901363 heterocyclic compound binding NA 9.70e-03 NA
GO:0043168 anion binding NA 1.41e-02 NA
GO:1901265 nucleoside phosphate binding NA 1.41e-02 NA
GO:0000166 nucleotide binding NA 1.41e-02 NA
GO:0043167 ion binding NA 1.45e-02 NA
GO:0017076 purine nucleotide binding NA 1.58e-02 NA
GO:0004672 protein kinase activity NA 1.58e-02 NA
GO:0070061 fructose binding NA 1.58e-02 NA
GO:0035639 purine ribonucleoside triphosphate bindi... NA 1.58e-02 NA
GO:0036094 small molecule binding NA 1.58e-02 NA
GO:0032553 ribonucleotide binding NA 1.58e-02 NA
GO:0042054 histone methyltransferase activity NA 1.58e-02 NA
GO:0051015 actin filament binding NA 1.58e-02 NA
GO:0016741 transferase activity, transferring one-c... NA 1.58e-02 NA
GO:0016627 oxidoreductase activity, acting on the C... NA 1.58e-02 NA
GO:0008168 methyltransferase activity NA 1.58e-02 NA
GO:0140640 catalytic activity, acting on a nucleic ... NA 1.62e-02 NA
GO:0032555 purine ribonucleotide binding NA 1.81e-02 NA
GO:0004674 protein serine/threonine kinase activity NA 2.11e-02 NA
GO:0019213 deacetylase activity NA 2.20e-02 NA
GO:0140939 histone H4 methyltransferase activity NA 2.20e-02 NA
GO:0008757 S-adenosylmethionine-dependent methyltra... NA 2.20e-02 NA
GO:0106310 protein serine kinase activity NA 2.20e-02 NA
GO:0030695 GTPase regulator activity NA 2.20e-02 NA
GO:0060589 nucleoside-triphosphatase regulator acti... NA 2.20e-02 NA
GO:0004386 helicase activity NA 2.20e-02 NA
GO:0003824 catalytic activity NA 2.42e-02 NA
GO:0140030 modification-dependent protein binding NA 2.64e-02 NA
GO:0097367 carbohydrate derivative binding NA 2.64e-02 NA
GO:0008276 protein methyltransferase activity NA 3.33e-02 NA
GO:0035242 protein-arginine omega-N asymmetric meth... NA 3.33e-02 NA
GO:0016740 transferase activity NA 3.80e-02 NA
GO:0008381 mechanosensitive monoatomic ion channel ... NA 3.80e-02 NA
GO:0008170 N-methyltransferase activity NA 4.66e-02 NA
GO:0003735 structural constituent of ribosome NA NA 1.61e-03
GO:0030527 structural constituent of chromatin NA NA 1.61e-03
GO:0046982 protein heterodimerization activity NA NA 2.59e-02

Functional enrichments of PCs using only DEGs


This table shows the enrichment FDR of Gene ontology terms in gene contibution to PCs
GO.ID Term positive.PC.1 negative.PC.1 positive.PC.2 negative.PC.2
GO:0005125 cytokine activity 3.56e-12 NA NA NA
GO:0005126 cytokine receptor binding 6.22e-12 NA NA NA
GO:0023026 MHC class II protein complex binding 3.00e-11 NA NA NA
GO:0005518 collagen binding 2.95e-10 NA NA NA
GO:0019207 kinase regulator activity 2.95e-10 NA NA NA
GO:0005525 GTP binding 1.30e-09 NA NA NA
GO:0019001 guanyl nucleotide binding 1.30e-09 NA NA NA
GO:0032561 guanyl ribonucleotide binding 1.30e-09 NA NA NA
GO:0003823 antigen binding 2.22e-09 NA NA NA
GO:0001664 G protein-coupled receptor binding 2.78e-07 NA NA NA
GO:0008013 beta-catenin binding 6.93e-05 NA NA NA
GO:0016491 oxidoreductase activity 2.80e-02 NA NA NA
GO:0046914 transition metal ion binding 2.80e-02 NA NA NA

Functional enrichments of HCPC clusters using only DEGs


This table shows the enrichment FDR of Gene ontology terms in gene contibution to HCPC clusters
GO.ID Term Cluster 1 Cluster 2 Cluster 3
GO:0008013 beta-catenin binding 6.14e-03 NA NA
GO:0140657 ATP-dependent activity 4.51e-02 NA NA
GO:0022804 active transmembrane transporter activit... 4.51e-02 NA NA

Values of options passed to the Functional Hunter main function

First column contains the option names; second column contains the given values for each option. Note that large data objects (e.g. expression results, organism table and custom annotation files) are not shown.
final_main_params
model_organism Human
annot_table NULL
input_gene_id ENSEMBL
custom NULL
enrich_dbs c("Reactome", "KEGG", "BP", "CC", "MF")
kegg_data_file /Users/marmtnez/Desktop/Master_Bioinfo/TFM/installed_software/ExpHunterSuite/inst/scripts/../../inst/kegg_data_files/hsa_KEGG.rds
enrich_methods ORA
annotation_source orgdb
pthreshold 0.1
qthreshold 0.2
cores 1
task_size 10
output_files /Users/marmtnez/Desktop/Master_Bioinfo/TFM/Results/functional/ctrl_vs_gtdup_fe
fc_colname mean_logFCs
universe NULL
clean_parentals FALSE
simplify FALSE
top_categories 50
sim_thr NULL
summary_common_name ancestor
clusters_flag TRUE